1 Background

In this report, we will study the Splicing noise for specific RBP/NMD projects. This is an extension of the analysis from Splicing_Analysis_Results.Rmd, please refer to that report to understand the methodology. Based on results from that analysis, we will focus this report in the following RBPs:

The figure that inspired these studied RBPs:

Studied RBPs

Figure 1.1: Studied RBPs

2 Studied metrics

Distances

An example of the novel junctions table obtained from the analysis can be seen in the following table:

Novel jun. ID Novel type Cluster Sequence Distance [bp]
363481 novel_acceptor case exon 18
961436 novel_acceptor control intron -46
358517 novel_acceptor case exon 53
2135689 novel_acceptor control exon 31
1603789 novel_acceptor case exon 24
790311 novel_acceptor case exon 5
422853 novel_acceptor control exon 4
1126415 novel_donor case intron -81
1478437 novel_acceptor control exon 3
2126164 novel_acceptor case intron -34

The distances graph is generated by counting the number of unique novel junctions at any given distance of the reference splicing site. From the list of novel junctions associated to common reference introns, we group by novel_type and cluster, count the number of entries for each distance within 30 bp into both intron and exon sequence, and represent the data in a histogram.

For each project, different graphical representations will be presented. First, we present a histogram of the different distance values between -30 and 30 bp, with the case bars stacked on top of the control bars:

However, this representation does not allow for an easy comparison between cases and controls because of the bar stacking. To do so, we split the graph in two more facets to represent each cluster by its own (notice the different Y-axis for the two rows):

If we focus on the difference in the number of unique novel junctions between cases and controls, the last graph represent the histogram resulting from subtracting the control distances from the case distances:

Distances (modulo 3)

To generate the modulo 3 graphs, we first filter by those distances smaller than 100 bp in either direction. Then, we group by novel_type and cluster, and calculate the distance in modulo 3 (i.e. the remainder from the division of the distance by 3). Once we have all novel junctions split in the four different categories with their distances in modulo 3, we calculate the percentage that each modulo 3 represents in each category. Thus, for each category:

\[ \text{mod.0 }\% = \frac{\# 0}{\#0 + \#1 + \#2}*100\%\qquad\quad \text{mod.1 }\% = \frac{\# 1}{\#0 + \#1 + \#2}*100\%\qquad\quad \text{mod.2 }\% = \frac{\# 2}{\#0 + \#1 + \#2}*100\% \]

Here, \(\#X\) represents the number of novel junctions at a modulo 3 distance equal to \(X\). For example, from the information of the following table, we can focus on the control acceptor group, where we observe three 0s, one 1 and one 2:

Novel jun. ID Novel type Cluster Sequence Distance [bp] Mod3 distance [bp]
case acceptor
1754423 novel_acceptor control exon 3 0
1863847 novel_acceptor case exon 78 0
2739925 novel_acceptor case exon 3 0
case donor
1360358 novel_acceptor control intron -82 1
control acceptor
2262507 novel_donor control intron -29 2
1050197 novel_donor case exon 7 1
973839 novel_acceptor case exon 24 0
317456 novel_acceptor control intron -27 0
2029914 novel_acceptor control exon 15 0
control donor
287795 novel_acceptor control intron -25 1

Thus, the calculated percentage are:

\[ \text{mod.0 }\% = 60\%\qquad\quad \text{mod.1 }\% = 20\%\qquad\quad \text{mod.2 }\% = 20\% \]

Additionally, we can further group the novel junctions by their intron/exon sequence, resulting a total of 8 categories, where the same calculation of percentages can be applied:

Novel jun. ID Novel type Cluster Sequence Distance [bp] Mod3 distance [bp]
case acceptor exon
1023682 novel_acceptor control exon 4 1
736164 novel_donor case exon 27 0
2730860 novel_donor case exon 48 0
case donor exon
2300571 novel_acceptor control intron -19 1
1502232 novel_acceptor control exon 5 2
control acceptor exon
1491329 novel_acceptor case exon 4 1
2559252 novel_donor control intron -10 1
405412 novel_donor control intron -7 1
control acceptor intron
2628084 novel_acceptor case exon 10 1
control donor exon
126904 novel_donor control intron -5 2
522911 novel_donor control exon 23 2
control donor intron
1297076 novel_acceptor case exon 5 2
427027 novel_acceptor control exon 4 1
453607 novel_donor control exon 10 1
857551 novel_donor control intron -4 1

With the previous tables in mind, we represent them in three different ways. The first one just represents the number of unique novel junctions for each modulo 3 distance where \(abs(distance) <= 100\).

We also represent the percentage that each that each distance in modulo 3 represents when grouped by novel_type (i.e. acceptor/donor) and cluster (i.e. case/control).

Lastly, we represent the same data as before but taking into consideration whether it is located in the intronic or exonic sequence:

Delta MaxEntScan Score

To represent the difference in MaxEntScan scores (MES), we subtract the MaxEntScan score of the annotated intron to the MaxEntScan score of a novel junction at each splice site. We obtain a table like the following, and represent the density plot of the different values for delta_ss5score and delta_ss3score:

\[ \text{Delta MES}^{5'} = \text{MES}_{ref}^{5'}-\text{MES}_{novel}^{5'}\qquad\qquad\text{Delta MES}^{3'} = \text{MES}_{ref}^{3'}-\text{MES}_{novel}^{3'} \]

Example table with the Delta MES data:

Novel jun. ID Ref. jun. ID Ref. ss5score Ref. ss3score Novel ss5score Novel ss3score Delta ss5score Delta ss3score
1935070 1935302 7.83 9.47 -5.84 9.47 13.67 0.00
2598431 2598425 9.09 7.77 -7.04 7.77 16.13 0.00
2826616 2826619 10.36 8.88 9.10 8.88 1.26 0.00
1533056 1533051 9.66 8.32 9.66 6.39 0.00 1.93
2745194 2745195 8.30 8.63 8.30 4.38 0.00 4.25
1263411 1263491 7.94 8.57 7.94 6.01 0.00 2.56
1274817 1274816 10.07 8.65 10.07 2.70 0.00 5.95
1042659 1042661 9.16 11.54 5.87 11.54 3.29 0.00
2675925 2675913 10.07 7.18 10.07 4.74 0.00 2.44
584316 584306 10.10 8.76 10.10 5.64 0.00 3.12

As for the visual representations, the difference between the MaxEntScan scores for each splice site is shown in the X-axis. The Y-axis represents the kernel density estimate (smoothed version of a histogram). The fill colour represents cases vs. controls.

Additionally, we can also represent the difference in the kernel density estimate between case and control:

MSR

The Mis-Splicing Ratio (MSR) is calculated in the data-analysis pipeline for each annotated intron found in the project samples. More information about the mis-splicing ratio can be found in the Splicing Analysis Results report. To visualize this data, we represent the density plot for MSR at the different splice sites (i.e. donor or acceptor). Example table with the MSR data:

Ref. jun, ID Cluster Ref. type MSR Donor MSR Acceptor
522301 case never 0.000 0.000
1673247 case never 0.000 0.000
799707 case never 0.000 0.000
164540 case never 0.000 0.000
561682 case both 0.008 0.016
1729913 case never 0.000 0.000
844081 case never 0.000 0.000
1863690 case never 0.000 0.000
2310284 control never 0.000 0.000
589320 control never 0.000 0.000

We represent both the distribution of mis-splicing ratio (MSR) at the donor site and the acceptor site. The X-axis represents the MSR, while the Y-axis represents the kernel density estimate.

Note that the distributions have a discontinuity at \(x=0.05\) to better represent all possible MSR values. In some cases, a discontinuity in the Y-axis will also be present if the difference between the two sample types exceeds a predefined threshold.

Stats

Under the Stats subsection, we will study different statistics of the annotated introns and novel junctions:

  • Unique annotated introns: number of annotated introns classified as never mis-spliced, mis-spliced at acceptor end, donor end or both. It is represented by cluster, so that we can study the variation in the number and percentage of never mis-spliced annotated introns.

  • Reads - annotated introns: total reads associated to annotated introns and the percentage that they represent against the total read depth.

  • Reads - novel junctions: total reads associated to novel junctions and the percentage that they represent against the total read depth. Results are separated by cluster.

3 Results

3.1 Splicing regulation

EFTUD2

ENCODE experiment summary:

Click for details

Information:

  • Target: EFTUD2
  • Category: Splicing_regulation
  • Assay: shRNA knockdown followed by RNA-seq
  • Nucleic acid type: polyadenylated mRNA
  • Lab: Brenton Gravely, UConn

Samples analysed:

  • 4 case samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 9.6 [1-1], 9.7 [2-1]
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 9.7
  • 4 control samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 9.6
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 9.7 [1-1], 9.3 [2-1]

Distances (N)

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions. Bars are stacked.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and cluster (same as colour).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Difference between the number of unique novel junctions from case samples and from control samples.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Modulo 3

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Number of unique novel junctions. Also represented as the text inside the bars.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control) and novel type (donor and acceptor).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control), novel type (donor and acceptor) and sequence (intronic and exonic).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and sequence (intronic vs. exonic).

Delta MaxEntScan

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Kernel density estimate (smoothed version of a histogram).
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Difference between the kernel density estimate for case samples and control samples.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

MSR

Expand details
  • X-Axis: The mis-splicing ratio.
  • Y-Axis: Kernel density estimate.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.
  • Notes: Distributions have a discontinuity at X = 0.05 to better represent all possible MSR values. In some cases, a discontinuity in the Y-axis is also present if the difference between the two sample types exceeds a predefined threshold.

Stats

Unique annotated introns
Mis-spliced site Cluster # Annotated introns # Ann. introns by splice site Percent [%]
acceptor case 109950 18270 16.62
acceptor control 109950 14086 12.81
both case 109950 11261 10.24
both control 109950 6434 5.85
donor case 109950 12456 11.33
donor control 109950 8886 8.08
never case 109950 67963 61.81
never control 109950 80544 73.26
Expand details
  • # Annotated introns: number of total annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Ann. introns by splice site: the number of annotated introns for the cluster and splice site.
  • Percent [%]: the percentage that the annotated introns in the splice site represent to the total number of introns in the cluster:
\[ \text{Percent [%]}=\frac{\text{# Ann. introns by splice site}}{\text{# Annotated introns}}*100\% \]
Reads - annotated introns
Cluster # Annotated introns # Reads in cluster # Ann. intron reads Percentage [%]
case 109950 95581047 57055044 59.69
control 109950 65858978 42355364 64.31
Expand details
  • # Annotated introns: number of common annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Ann. intron reads: reads associated to the annotated introns in the cluster. Only common introns are being counted.
  • Percent [%]: the percentage that the annotated intron reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Ann. intron reads}}{\text{# Reads in cluster}}*100\% \]
Reads - novel junctions
Cluster Novel type # Novel junctions # Novel junc. in splice site # Reads in cluster # Novel junc. reads Percentage [%]
case novel_acceptor 73698 40563 95581047 131151 0.14
case novel_donor 73698 33135 95581047 109513 0.11
control novel_acceptor 45976 26222 65858978 79648 0.12
control novel_donor 45976 19754 65858978 59477 0.09
Expand details
  • # Novel junctions: total number of novel junctions for that particular cluster.
  • # Novel junc. in splice site: total number of novel junctions for that particular splice site in the cluster.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Novel junc. reads: reads associated to the novel junctions in the cluster and splice site.
  • Percent [%]: the percentage that the novel junction reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Novel junc. reads}}{\text{# Reads in cluster}}*100\% \]

U2AF2

ENCODE experiment summary:

Click for details

Information:

  • Target: U2AF2
  • Category: Splicing_regulation
  • Assay: shRNA knockdown followed by RNA-seq
  • Nucleic acid type: polyadenylated mRNA
  • Lab: Brenton Gravely, UConn

Samples analysed:

  • 4 case samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 9.8
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 9.2 [2-1], 9.0 [1-1]
  • 4 control samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 9.7 [1-1], 9.8 [2-1]
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 9.2

Distances (N)

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions. Bars are stacked.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and cluster (same as colour).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Difference between the number of unique novel junctions from case samples and from control samples.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Modulo 3

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Number of unique novel junctions. Also represented as the text inside the bars.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control) and novel type (donor and acceptor).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control), novel type (donor and acceptor) and sequence (intronic and exonic).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and sequence (intronic vs. exonic).

Delta MaxEntScan

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Kernel density estimate (smoothed version of a histogram).
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Difference between the kernel density estimate for case samples and control samples.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

MSR

Expand details
  • X-Axis: The mis-splicing ratio.
  • Y-Axis: Kernel density estimate.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.
  • Notes: Distributions have a discontinuity at X = 0.05 to better represent all possible MSR values. In some cases, a discontinuity in the Y-axis is also present if the difference between the two sample types exceeds a predefined threshold.

Stats

Unique annotated introns
Mis-spliced site Cluster # Annotated introns # Ann. introns by splice site Percent [%]
acceptor case 109950 19769 17.98
acceptor control 109950 13665 12.43
both case 109950 9004 8.19
both control 109950 6063 5.51
donor case 109950 9367 8.52
donor control 109950 8655 7.87
never case 109950 71810 65.31
never control 109950 81567 74.19
Expand details
  • # Annotated introns: number of total annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Ann. introns by splice site: the number of annotated introns for the cluster and splice site.
  • Percent [%]: the percentage that the annotated introns in the splice site represent to the total number of introns in the cluster:
\[ \text{Percent [%]}=\frac{\text{# Ann. introns by splice site}}{\text{# Annotated introns}}*100\% \]
Reads - annotated introns
Cluster # Annotated introns # Reads in cluster # Ann. intron reads Percentage [%]
case 109950 139108128 66096990 47.51
control 109950 103415982 62586996 60.52
Expand details
  • # Annotated introns: number of common annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Ann. intron reads: reads associated to the annotated introns in the cluster. Only common introns are being counted.
  • Percent [%]: the percentage that the annotated intron reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Ann. intron reads}}{\text{# Reads in cluster}}*100\% \]
Reads - novel junctions
Cluster Novel type # Novel junctions # Novel junc. in splice site # Reads in cluster # Novel junc. reads Percentage [%]
case novel_acceptor 65546 40372 139108128 186928 0.13
case novel_donor 65546 25174 139108128 109366 0.08
control novel_acceptor 44508 25403 103415982 108110 0.10
control novel_donor 44508 19105 103415982 77954 0.08
Expand details
  • # Novel junctions: total number of novel junctions for that particular cluster.
  • # Novel junc. in splice site: total number of novel junctions for that particular splice site in the cluster.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Novel junc. reads: reads associated to the novel junctions in the cluster and splice site.
  • Percent [%]: the percentage that the novel junction reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Novel junc. reads}}{\text{# Reads in cluster}}*100\% \]

U2AF1

ENCODE experiment summary:

Click for details

Information:

  • Target: U2AF1
  • Category: Splicing_regulation
  • Assay: shRNA knockdown followed by RNA-seq
  • Nucleic acid type: polyadenylated mRNA
  • Lab: Brenton Gravely, UConn

Samples analysed:

  • 4 case samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 9.9
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 9.3 [1-1], 9.0 [2-1]
  • 4 control samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 10
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 9.2

Distances (N)

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions. Bars are stacked.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and cluster (same as colour).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Difference between the number of unique novel junctions from case samples and from control samples.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Modulo 3

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Number of unique novel junctions. Also represented as the text inside the bars.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control) and novel type (donor and acceptor).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control), novel type (donor and acceptor) and sequence (intronic and exonic).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and sequence (intronic vs. exonic).

Delta MaxEntScan

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Kernel density estimate (smoothed version of a histogram).
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Difference between the kernel density estimate for case samples and control samples.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

MSR

Expand details
  • X-Axis: The mis-splicing ratio.
  • Y-Axis: Kernel density estimate.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.
  • Notes: Distributions have a discontinuity at X = 0.05 to better represent all possible MSR values. In some cases, a discontinuity in the Y-axis is also present if the difference between the two sample types exceeds a predefined threshold.

Stats

Unique annotated introns
Mis-spliced site Cluster # Annotated introns # Ann. introns by splice site Percent [%]
acceptor case 109950 21559 19.61
acceptor control 109950 15553 14.15
both case 109950 11286 10.26
both control 109950 7235 6.58
donor case 109950 10515 9.56
donor control 109950 9359 8.51
never case 109950 66590 60.56
never control 109950 77803 70.76
Expand details
  • # Annotated introns: number of total annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Ann. introns by splice site: the number of annotated introns for the cluster and splice site.
  • Percent [%]: the percentage that the annotated introns in the splice site represent to the total number of introns in the cluster:
\[ \text{Percent [%]}=\frac{\text{# Ann. introns by splice site}}{\text{# Annotated introns}}*100\% \]
Reads - annotated introns
Cluster # Annotated introns # Reads in cluster # Ann. intron reads Percentage [%]
case 109950 131286007 67739458 51.60
control 109950 102950731 59580485 57.87
Expand details
  • # Annotated introns: number of common annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Ann. intron reads: reads associated to the annotated introns in the cluster. Only common introns are being counted.
  • Percent [%]: the percentage that the annotated intron reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Ann. intron reads}}{\text{# Reads in cluster}}*100\% \]
Reads - novel junctions
Cluster Novel type # Novel junctions # Novel junc. in splice site # Reads in cluster # Novel junc. reads Percentage [%]
case novel_acceptor 78217 47601 131286007 196876 0.15
case novel_donor 78217 30616 131286007 123442 0.09
control novel_acceptor 51788 29903 102950731 108941 0.11
control novel_donor 51788 21885 102950731 78812 0.08
Expand details
  • # Novel junctions: total number of novel junctions for that particular cluster.
  • # Novel junc. in splice site: total number of novel junctions for that particular splice site in the cluster.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Novel junc. reads: reads associated to the novel junctions in the cluster and splice site.
  • Percent [%]: the percentage that the novel junction reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Novel junc. reads}}{\text{# Reads in cluster}}*100\% \]

HNRNPC

ENCODE experiment summary:

Click for details

Information:

  • Target: HNRNPC
  • Category: Splicing_regulation
  • Assay: shRNA knockdown followed by RNA-seq
  • Nucleic acid type: polyadenylated mRNA
  • Lab: Brenton Gravely, UConn

Samples analysed:

  • 4 case samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 9.9
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 9.6 [1-1], 9.4 [2-1]
  • 4 control samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 9.9 [1-1], 9.8 [2-1]
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 10.0 [2-1], 9.8 [1-1]

Distances (N)

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions. Bars are stacked.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and cluster (same as colour).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Difference between the number of unique novel junctions from case samples and from control samples.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Modulo 3

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Number of unique novel junctions. Also represented as the text inside the bars.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control) and novel type (donor and acceptor).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control), novel type (donor and acceptor) and sequence (intronic and exonic).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and sequence (intronic vs. exonic).

Delta MaxEntScan

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Kernel density estimate (smoothed version of a histogram).
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Difference between the kernel density estimate for case samples and control samples.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

MSR

Expand details
  • X-Axis: The mis-splicing ratio.
  • Y-Axis: Kernel density estimate.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.
  • Notes: Distributions have a discontinuity at X = 0.05 to better represent all possible MSR values. In some cases, a discontinuity in the Y-axis is also present if the difference between the two sample types exceeds a predefined threshold.

Stats

Unique annotated introns
Mis-spliced site Cluster # Annotated introns # Ann. introns by splice site Percent [%]
acceptor case 109950 18610 16.93
acceptor control 109950 15717 14.29
both case 109950 12184 11.08
both control 109950 7109 6.47
donor case 109950 10436 9.49
donor control 109950 9288 8.45
never case 109950 68720 62.50
never control 109950 77836 70.79
Expand details
  • # Annotated introns: number of total annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Ann. introns by splice site: the number of annotated introns for the cluster and splice site.
  • Percent [%]: the percentage that the annotated introns in the splice site represent to the total number of introns in the cluster:
\[ \text{Percent [%]}=\frac{\text{# Ann. introns by splice site}}{\text{# Annotated introns}}*100\% \]
Reads - annotated introns
Cluster # Annotated introns # Reads in cluster # Ann. intron reads Percentage [%]
case 109950 87390817 47804029 54.70
control 109950 90031602 55948250 62.14
Expand details
  • # Annotated introns: number of common annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Ann. intron reads: reads associated to the annotated introns in the cluster. Only common introns are being counted.
  • Percent [%]: the percentage that the annotated intron reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Ann. intron reads}}{\text{# Reads in cluster}}*100\% \]
Reads - novel junctions
Cluster Novel type # Novel junctions # Novel junc. in splice site # Reads in cluster # Novel junc. reads Percentage [%]
case novel_acceptor 78313 45366 87390817 185465 0.21
case novel_donor 78313 32947 87390817 143669 0.16
control novel_acceptor 51396 29865 90031602 102086 0.11
control novel_donor 51396 21531 90031602 72824 0.08
Expand details
  • # Novel junctions: total number of novel junctions for that particular cluster.
  • # Novel junc. in splice site: total number of novel junctions for that particular splice site in the cluster.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Novel junc. reads: reads associated to the novel junctions in the cluster and splice site.
  • Percent [%]: the percentage that the novel junction reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Novel junc. reads}}{\text{# Reads in cluster}}*100\% \]

DAZAP1

ENCODE experiment summary:

Click for details

Information:

  • Target: DAZAP1
  • Category: Splicing_regulation
  • Assay: shRNA knockdown followed by RNA-seq
  • Nucleic acid type: polyadenylated mRNA
  • Lab: Brenton Gravely, UConn

Samples analysed:

  • 4 case samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 9.6
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 9.5 [2-1], 9.3 [1-1]
  • 4 control samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 9.7 [1-1], 9.6 [2-1]
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 9.5 [1-1], 9.3 [2-1]

Distances (N)

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions. Bars are stacked.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and cluster (same as colour).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Difference between the number of unique novel junctions from case samples and from control samples.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Modulo 3

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Number of unique novel junctions. Also represented as the text inside the bars.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control) and novel type (donor and acceptor).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control), novel type (donor and acceptor) and sequence (intronic and exonic).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and sequence (intronic vs. exonic).

Delta MaxEntScan

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Kernel density estimate (smoothed version of a histogram).
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Difference between the kernel density estimate for case samples and control samples.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

MSR

Expand details
  • X-Axis: The mis-splicing ratio.
  • Y-Axis: Kernel density estimate.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.
  • Notes: Distributions have a discontinuity at X = 0.05 to better represent all possible MSR values. In some cases, a discontinuity in the Y-axis is also present if the difference between the two sample types exceeds a predefined threshold.

Stats

Unique annotated introns
Mis-spliced site Cluster # Annotated introns # Ann. introns by splice site Percent [%]
acceptor case 109950 17425 15.85
acceptor control 109950 17890 16.27
both case 109950 9299 8.46
both control 109950 9824 8.93
donor case 109950 10320 9.39
donor control 109950 10512 9.56
never case 109950 72906 66.31
never control 109950 71724 65.23
Expand details
  • # Annotated introns: number of total annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Ann. introns by splice site: the number of annotated introns for the cluster and splice site.
  • Percent [%]: the percentage that the annotated introns in the splice site represent to the total number of introns in the cluster:
\[ \text{Percent [%]}=\frac{\text{# Ann. introns by splice site}}{\text{# Annotated introns}}*100\% \]
Reads - annotated introns
Cluster # Annotated introns # Reads in cluster # Ann. intron reads Percentage [%]
case 109950 113084161 72796158 64.37
control 109950 123546347 80521666 65.18
Expand details
  • # Annotated introns: number of common annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Ann. intron reads: reads associated to the annotated introns in the cluster. Only common introns are being counted.
  • Percent [%]: the percentage that the annotated intron reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Ann. intron reads}}{\text{# Reads in cluster}}*100\% \]
Reads - novel junctions
Cluster Novel type # Novel junctions # Novel junc. in splice site # Reads in cluster # Novel junc. reads Percentage [%]
case novel_acceptor 63140 36386 113084161 137440 0.12
case novel_donor 63140 26754 113084161 103469 0.09
control novel_acceptor 66081 38025 123546347 143463 0.12
control novel_donor 66081 28056 123546347 107709 0.09
Expand details
  • # Novel junctions: total number of novel junctions for that particular cluster.
  • # Novel junc. in splice site: total number of novel junctions for that particular splice site in the cluster.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Novel junc. reads: reads associated to the novel junctions in the cluster and splice site.
  • Percent [%]: the percentage that the novel junction reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Novel junc. reads}}{\text{# Reads in cluster}}*100\% \]

ZRANB2

ENCODE experiment summary:

Click for details

Information:

  • Target: ZRANB2
  • Category: Splicing_regulation
  • Assay: shRNA knockdown followed by RNA-seq
  • Nucleic acid type: polyadenylated mRNA
  • Lab: Brenton Gravely, UConn

Samples analysed:

  • 4 case samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 9.6 [1-1], 9.5 [2-1]
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 9.2 [1-1], 9.6 [2-1]
  • 4 control samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 9.4 [1-1], 9.5 [2-1]
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 9.5 [1-1], 9.3 [2-1]

Distances (N)

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions. Bars are stacked.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and cluster (same as colour).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Difference between the number of unique novel junctions from case samples and from control samples.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Modulo 3

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Number of unique novel junctions. Also represented as the text inside the bars.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control) and novel type (donor and acceptor).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control), novel type (donor and acceptor) and sequence (intronic and exonic).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and sequence (intronic vs. exonic).

Delta MaxEntScan

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Kernel density estimate (smoothed version of a histogram).
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Difference between the kernel density estimate for case samples and control samples.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

MSR

Expand details
  • X-Axis: The mis-splicing ratio.
  • Y-Axis: Kernel density estimate.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.
  • Notes: Distributions have a discontinuity at X = 0.05 to better represent all possible MSR values. In some cases, a discontinuity in the Y-axis is also present if the difference between the two sample types exceeds a predefined threshold.

Stats

Unique annotated introns
Mis-spliced site Cluster # Annotated introns # Ann. introns by splice site Percent [%]
acceptor case 109950 15859 14.42
acceptor control 109950 16478 14.99
both case 109950 8045 7.32
both control 109950 8585 7.81
donor case 109950 10180 9.26
donor control 109950 10050 9.14
never case 109950 75866 69.00
never control 109950 74837 68.06
Expand details
  • # Annotated introns: number of total annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Ann. introns by splice site: the number of annotated introns for the cluster and splice site.
  • Percent [%]: the percentage that the annotated introns in the splice site represent to the total number of introns in the cluster:
\[ \text{Percent [%]}=\frac{\text{# Ann. introns by splice site}}{\text{# Annotated introns}}*100\% \]
Reads - annotated introns
Cluster # Annotated introns # Reads in cluster # Ann. intron reads Percentage [%]
case 109950 91520968 56599674 61.84
control 109950 95867805 61574898 64.23
Expand details
  • # Annotated introns: number of common annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Ann. intron reads: reads associated to the annotated introns in the cluster. Only common introns are being counted.
  • Percent [%]: the percentage that the annotated intron reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Ann. intron reads}}{\text{# Reads in cluster}}*100\% \]
Reads - novel junctions
Cluster Novel type # Novel junctions # Novel junc. in splice site # Reads in cluster # Novel junc. reads Percentage [%]
case novel_acceptor 55870 31557 91520968 106523 0.12
case novel_donor 55870 24313 91520968 84947 0.09
control novel_acceptor 58648 33384 95867805 114395 0.12
control novel_donor 58648 25264 95867805 86835 0.09
Expand details
  • # Novel junctions: total number of novel junctions for that particular cluster.
  • # Novel junc. in splice site: total number of novel junctions for that particular splice site in the cluster.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Novel junc. reads: reads associated to the novel junctions in the cluster and splice site.
  • Percent [%]: the percentage that the novel junction reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Novel junc. reads}}{\text{# Reads in cluster}}*100\% \]

SND1

ENCODE experiment summary:

Click for details

Information:

  • Target: SND1
  • Category: Splicing_regulation
  • Assay: shRNA knockdown followed by RNA-seq
  • Nucleic acid type: polyadenylated mRNA
  • Lab: Brenton Gravely, UConn

Samples analysed:

  • 4 case samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 9.6
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 9.4 [2-1], 9.3 [1-1]
  • 4 control samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 9.4 [1-1], 9.5 [2-1]
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 9.4 [1-1], 9.3 [2-1]

Distances (N)

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions. Bars are stacked.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and cluster (same as colour).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Difference between the number of unique novel junctions from case samples and from control samples.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Modulo 3

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Number of unique novel junctions. Also represented as the text inside the bars.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control) and novel type (donor and acceptor).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control), novel type (donor and acceptor) and sequence (intronic and exonic).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and sequence (intronic vs. exonic).

Delta MaxEntScan

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Kernel density estimate (smoothed version of a histogram).
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Difference between the kernel density estimate for case samples and control samples.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

MSR

Expand details
  • X-Axis: The mis-splicing ratio.
  • Y-Axis: Kernel density estimate.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.
  • Notes: Distributions have a discontinuity at X = 0.05 to better represent all possible MSR values. In some cases, a discontinuity in the Y-axis is also present if the difference between the two sample types exceeds a predefined threshold.

Stats

Unique annotated introns
Mis-spliced site Cluster # Annotated introns # Ann. introns by splice site Percent [%]
acceptor case 109950 15020 13.66
acceptor control 109950 15541 14.13
both case 109950 7748 7.05
both control 109950 7891 7.18
donor case 109950 9413 8.56
donor control 109950 9775 8.89
never case 109950 77769 70.73
never control 109950 76743 69.80
Expand details
  • # Annotated introns: number of total annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Ann. introns by splice site: the number of annotated introns for the cluster and splice site.
  • Percent [%]: the percentage that the annotated introns in the splice site represent to the total number of introns in the cluster:
\[ \text{Percent [%]}=\frac{\text{# Ann. introns by splice site}}{\text{# Annotated introns}}*100\% \]
Reads - annotated introns
Cluster # Annotated introns # Reads in cluster # Ann. intron reads Percentage [%]
case 109950 81752442 50647498 61.95
control 109950 88157283 55672338 63.15
Expand details
  • # Annotated introns: number of common annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Ann. intron reads: reads associated to the annotated introns in the cluster. Only common introns are being counted.
  • Percent [%]: the percentage that the annotated intron reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Ann. intron reads}}{\text{# Reads in cluster}}*100\% \]
Reads - novel junctions
Cluster Novel type # Novel junctions # Novel junc. in splice site # Reads in cluster # Novel junc. reads Percentage [%]
case novel_acceptor 52661 29889 81752442 96038 0.12
case novel_donor 52661 22772 81752442 74037 0.09
control novel_acceptor 54588 30897 88157283 100494 0.11
control novel_donor 54588 23691 88157283 79025 0.09
Expand details
  • # Novel junctions: total number of novel junctions for that particular cluster.
  • # Novel junc. in splice site: total number of novel junctions for that particular splice site in the cluster.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Novel junc. reads: reads associated to the novel junctions in the cluster and splice site.
  • Percent [%]: the percentage that the novel junction reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Novel junc. reads}}{\text{# Reads in cluster}}*100\% \]

SRSF5

ENCODE experiment summary:

Click for details

Information:

  • Target: SRSF5
  • Category: Splicing_regulation
  • Assay: shRNA knockdown followed by RNA-seq
  • Nucleic acid type: polyadenylated mRNA
  • Lab: Brenton Gravely, UConn

Samples analysed:

  • 4 case samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 9.5 [1-1], 9.7 [2-1]
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 9.3 [1-1], 8.9 [2-1]
  • 4 control samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 9.7 [1-1], 9.6 [2-1]
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 9.0 [1-1], 9.2 [2-1]

Distances (N)

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions. Bars are stacked.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and cluster (same as colour).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Difference between the number of unique novel junctions from case samples and from control samples.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Modulo 3

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Number of unique novel junctions. Also represented as the text inside the bars.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control) and novel type (donor and acceptor).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control), novel type (donor and acceptor) and sequence (intronic and exonic).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and sequence (intronic vs. exonic).

Delta MaxEntScan

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Kernel density estimate (smoothed version of a histogram).
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Difference between the kernel density estimate for case samples and control samples.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

MSR

Expand details
  • X-Axis: The mis-splicing ratio.
  • Y-Axis: Kernel density estimate.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.
  • Notes: Distributions have a discontinuity at X = 0.05 to better represent all possible MSR values. In some cases, a discontinuity in the Y-axis is also present if the difference between the two sample types exceeds a predefined threshold.

Stats

Unique annotated introns
Mis-spliced site Cluster # Annotated introns # Ann. introns by splice site Percent [%]
acceptor case 109950 17613 16.02
acceptor control 109950 17986 16.36
both case 109950 9380 8.53
both control 109950 9527 8.66
donor case 109950 10326 9.39
donor control 109950 10487 9.54
never case 109950 72631 66.06
never control 109950 71950 65.44
Expand details
  • # Annotated introns: number of total annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Ann. introns by splice site: the number of annotated introns for the cluster and splice site.
  • Percent [%]: the percentage that the annotated introns in the splice site represent to the total number of introns in the cluster:
\[ \text{Percent [%]}=\frac{\text{# Ann. introns by splice site}}{\text{# Annotated introns}}*100\% \]
Reads - annotated introns
Cluster # Annotated introns # Reads in cluster # Ann. intron reads Percentage [%]
case 109950 100754176 64596002 64.11
control 109950 138180087 86870723 62.87
Expand details
  • # Annotated introns: number of common annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Ann. intron reads: reads associated to the annotated introns in the cluster. Only common introns are being counted.
  • Percent [%]: the percentage that the annotated intron reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Ann. intron reads}}{\text{# Reads in cluster}}*100\% \]
Reads - novel junctions
Cluster Novel type # Novel junctions # Novel junc. in splice site # Reads in cluster # Novel junc. reads Percentage [%]
case novel_acceptor 63644 36881 100754176 128834 0.13
case novel_donor 63644 26763 100754176 95041 0.09
control novel_acceptor 65324 37777 138180087 149333 0.11
control novel_donor 65324 27547 138180087 112111 0.08
Expand details
  • # Novel junctions: total number of novel junctions for that particular cluster.
  • # Novel junc. in splice site: total number of novel junctions for that particular splice site in the cluster.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Novel junc. reads: reads associated to the novel junctions in the cluster and splice site.
  • Percent [%]: the percentage that the novel junction reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Novel junc. reads}}{\text{# Reads in cluster}}*100\% \]

NONO

ENCODE experiment summary:

Click for details

Information:

  • Target: NONO
  • Category: Splicing_regulation
  • Assay: shRNA knockdown followed by RNA-seq
  • Nucleic acid type: polyadenylated mRNA
  • Lab: Brenton Gravely, UConn

Samples analysed:

  • 4 case samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 9.7 [1-1], 9.6 [2-1]
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 9.6 [2-1], 9.5 [1-1]
  • 4 control samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 9.6 [1-1], 9.8 [2-1]
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 9.7 [1-1], 9.3 [2-1]

Distances (N)

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions. Bars are stacked.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and cluster (same as colour).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Difference between the number of unique novel junctions from case samples and from control samples.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Modulo 3

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Number of unique novel junctions. Also represented as the text inside the bars.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control) and novel type (donor and acceptor).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control), novel type (donor and acceptor) and sequence (intronic and exonic).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and sequence (intronic vs. exonic).

Delta MaxEntScan

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Kernel density estimate (smoothed version of a histogram).
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Difference between the kernel density estimate for case samples and control samples.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

MSR

Expand details
  • X-Axis: The mis-splicing ratio.
  • Y-Axis: Kernel density estimate.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.
  • Notes: Distributions have a discontinuity at X = 0.05 to better represent all possible MSR values. In some cases, a discontinuity in the Y-axis is also present if the difference between the two sample types exceeds a predefined threshold.

Stats

Unique annotated introns
Mis-spliced site Cluster # Annotated introns # Ann. introns by splice site Percent [%]
acceptor case 109950 18788 17.09
acceptor control 109950 15810 14.38
both case 109950 10451 9.51
both control 109950 7681 6.99
donor case 109950 10916 9.93
donor control 109950 9693 8.82
never case 109950 69795 63.48
never control 109950 76766 69.82
Expand details
  • # Annotated introns: number of total annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Ann. introns by splice site: the number of annotated introns for the cluster and splice site.
  • Percent [%]: the percentage that the annotated introns in the splice site represent to the total number of introns in the cluster:
\[ \text{Percent [%]}=\frac{\text{# Ann. introns by splice site}}{\text{# Annotated introns}}*100\% \]
Reads - annotated introns
Cluster # Annotated introns # Reads in cluster # Ann. intron reads Percentage [%]
case 109950 98785090 66624975 67.44
control 109950 78934064 51369435 65.08
Expand details
  • # Annotated introns: number of common annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Ann. intron reads: reads associated to the annotated introns in the cluster. Only common introns are being counted.
  • Percent [%]: the percentage that the annotated intron reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Ann. intron reads}}{\text{# Reads in cluster}}*100\% \]
Reads - novel junctions
Cluster Novel type # Novel junctions # Novel junc. in splice site # Reads in cluster # Novel junc. reads Percentage [%]
case novel_acceptor 70863 40733 98785090 138015 0.14
case novel_donor 70863 30130 98785090 105799 0.11
control novel_acceptor 53565 30753 78934064 94553 0.12
control novel_donor 53565 22812 78934064 71888 0.09
Expand details
  • # Novel junctions: total number of novel junctions for that particular cluster.
  • # Novel junc. in splice site: total number of novel junctions for that particular splice site in the cluster.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Novel junc. reads: reads associated to the novel junctions in the cluster and splice site.
  • Percent [%]: the percentage that the novel junction reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Novel junc. reads}}{\text{# Reads in cluster}}*100\% \]

ADAR

ENCODE experiment summary:

Click for details

Information:

  • Target: ADAR
  • Category: Splicing_regulation
  • Assay: shRNA knockdown followed by RNA-seq
  • Nucleic acid type: polyadenylated mRNA
  • Lab: Brenton Gravely, UConn

Samples analysed:

  • 4 case samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 9.9 [2-1], 9.8 [1-1]
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 9.8 [1-1], 9.5 [2-1]
  • 4 control samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 9.9 [1-1], 9.8 [2-1]
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 9.7 [1-1], 9.8 [2-1]

Distances (N)

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions. Bars are stacked.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and cluster (same as colour).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Difference between the number of unique novel junctions from case samples and from control samples.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Modulo 3

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Number of unique novel junctions. Also represented as the text inside the bars.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control) and novel type (donor and acceptor).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control), novel type (donor and acceptor) and sequence (intronic and exonic).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and sequence (intronic vs. exonic).

Delta MaxEntScan

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Kernel density estimate (smoothed version of a histogram).
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Difference between the kernel density estimate for case samples and control samples.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

MSR

Expand details
  • X-Axis: The mis-splicing ratio.
  • Y-Axis: Kernel density estimate.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.
  • Notes: Distributions have a discontinuity at X = 0.05 to better represent all possible MSR values. In some cases, a discontinuity in the Y-axis is also present if the difference between the two sample types exceeds a predefined threshold.

Stats

Unique annotated introns
Mis-spliced site Cluster # Annotated introns # Ann. introns by splice site Percent [%]
acceptor case 109950 15760 14.33
acceptor control 109950 14567 13.25
both case 109950 7073 6.43
both control 109950 6396 5.82
donor case 109950 8872 8.07
donor control 109950 8766 7.97
never case 109950 78245 71.16
never control 109950 80221 72.96
Expand details
  • # Annotated introns: number of total annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Ann. introns by splice site: the number of annotated introns for the cluster and splice site.
  • Percent [%]: the percentage that the annotated introns in the splice site represent to the total number of introns in the cluster:
\[ \text{Percent [%]}=\frac{\text{# Ann. introns by splice site}}{\text{# Annotated introns}}*100\% \]
Reads - annotated introns
Cluster # Annotated introns # Reads in cluster # Ann. intron reads Percentage [%]
case 109950 75910349 44094079 58.09
control 109950 74988044 45380161 60.52
Expand details
  • # Annotated introns: number of common annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Ann. intron reads: reads associated to the annotated introns in the cluster. Only common introns are being counted.
  • Percent [%]: the percentage that the annotated intron reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Ann. intron reads}}{\text{# Reads in cluster}}*100\% \]
Reads - novel junctions
Cluster Novel type # Novel junctions # Novel junc. in splice site # Reads in cluster # Novel junc. reads Percentage [%]
case novel_acceptor 50693 29843 75910349 93607 0.12
case novel_donor 50693 20850 75910349 65790 0.09
control novel_acceptor 46756 27067 74988044 85697 0.11
control novel_donor 46756 19689 74988044 61378 0.08
Expand details
  • # Novel junctions: total number of novel junctions for that particular cluster.
  • # Novel junc. in splice site: total number of novel junctions for that particular splice site in the cluster.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Novel junc. reads: reads associated to the novel junctions in the cluster and splice site.
  • Percent [%]: the percentage that the novel junction reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Novel junc. reads}}{\text{# Reads in cluster}}*100\% \]

HNRNPU

ENCODE experiment summary:

Click for details

Information:

  • Target: HNRNPU
  • Category: Splicing_regulation
  • Assay: shRNA knockdown followed by RNA-seq
  • Nucleic acid type: polyadenylated mRNA
  • Lab: Brenton Gravely, UConn

Samples analysed:

  • 4 case samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 9.9 [1-1], 9.8 [2-1]
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 9.4 [2-1], 7.0 [1-1]
  • 4 control samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 9.9 [1-1], 9.8 [2-1]
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 9.8 [1-1], 10.0 [2-1]

Distances (N)

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions. Bars are stacked.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and cluster (same as colour).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Difference between the number of unique novel junctions from case samples and from control samples.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Modulo 3

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Number of unique novel junctions. Also represented as the text inside the bars.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control) and novel type (donor and acceptor).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control), novel type (donor and acceptor) and sequence (intronic and exonic).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and sequence (intronic vs. exonic).

Delta MaxEntScan

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Kernel density estimate (smoothed version of a histogram).
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Difference between the kernel density estimate for case samples and control samples.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

MSR

Expand details
  • X-Axis: The mis-splicing ratio.
  • Y-Axis: Kernel density estimate.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.
  • Notes: Distributions have a discontinuity at X = 0.05 to better represent all possible MSR values. In some cases, a discontinuity in the Y-axis is also present if the difference between the two sample types exceeds a predefined threshold.

Stats

Unique annotated introns
Mis-spliced site Cluster # Annotated introns # Ann. introns by splice site Percent [%]
acceptor case 109950 18354 16.69
acceptor control 109950 17072 15.53
both case 109950 9600 8.73
both control 109950 8843 8.04
donor case 109950 11041 10.04
donor control 109950 10025 9.12
never case 109950 70955 64.53
never control 109950 74010 67.31
Expand details
  • # Annotated introns: number of total annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Ann. introns by splice site: the number of annotated introns for the cluster and splice site.
  • Percent [%]: the percentage that the annotated introns in the splice site represent to the total number of introns in the cluster:
\[ \text{Percent [%]}=\frac{\text{# Ann. introns by splice site}}{\text{# Annotated introns}}*100\% \]
Reads - annotated introns
Cluster # Annotated introns # Reads in cluster # Ann. intron reads Percentage [%]
case 109950 107100947 67220366 62.76
control 109950 104974265 68643820 65.39
Expand details
  • # Annotated introns: number of common annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Ann. intron reads: reads associated to the annotated introns in the cluster. Only common introns are being counted.
  • Percent [%]: the percentage that the annotated intron reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Ann. intron reads}}{\text{# Reads in cluster}}*100\% \]
Reads - novel junctions
Cluster Novel type # Novel junctions # Novel junc. in splice site # Reads in cluster # Novel junc. reads Percentage [%]
case novel_acceptor 66654 38375 107100947 136058 0.13
case novel_donor 66654 28279 107100947 104238 0.10
control novel_acceptor 60402 35054 104974265 124731 0.12
control novel_donor 60402 25348 104974265 90643 0.09
Expand details
  • # Novel junctions: total number of novel junctions for that particular cluster.
  • # Novel junc. in splice site: total number of novel junctions for that particular splice site in the cluster.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Novel junc. reads: reads associated to the novel junctions in the cluster and splice site.
  • Percent [%]: the percentage that the novel junction reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Novel junc. reads}}{\text{# Reads in cluster}}*100\% \]

MATR3

ENCODE experiment summary:

Click for details

Information:

  • Target: MATR3
  • Category: Splicing_regulation
  • Assay: shRNA knockdown followed by RNA-seq
  • Nucleic acid type: polyadenylated mRNA
  • Lab: Brenton Gravely, UConn

Samples analysed:

  • 4 case samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 9.3 [1-1], 9.5 [2-1]
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 9
  • 4 control samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 8.9
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 9.0 [1-1], 9.2 [2-1]

Distances (N)

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions. Bars are stacked.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and cluster (same as colour).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Difference between the number of unique novel junctions from case samples and from control samples.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Modulo 3

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Number of unique novel junctions. Also represented as the text inside the bars.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control) and novel type (donor and acceptor).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control), novel type (donor and acceptor) and sequence (intronic and exonic).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and sequence (intronic vs. exonic).

Delta MaxEntScan

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Kernel density estimate (smoothed version of a histogram).
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Difference between the kernel density estimate for case samples and control samples.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

MSR

Expand details
  • X-Axis: The mis-splicing ratio.
  • Y-Axis: Kernel density estimate.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.
  • Notes: Distributions have a discontinuity at X = 0.05 to better represent all possible MSR values. In some cases, a discontinuity in the Y-axis is also present if the difference between the two sample types exceeds a predefined threshold.

Stats

Unique annotated introns
Mis-spliced site Cluster # Annotated introns # Ann. introns by splice site Percent [%]
acceptor case 109950 18183 16.54
acceptor control 109950 16339 14.86
both case 109950 10773 9.80
both control 109950 7938 7.22
donor case 109950 10867 9.88
donor control 109950 9806 8.92
never case 109950 70127 63.78
never control 109950 75867 69.00
Expand details
  • # Annotated introns: number of total annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Ann. introns by splice site: the number of annotated introns for the cluster and splice site.
  • Percent [%]: the percentage that the annotated introns in the splice site represent to the total number of introns in the cluster:
\[ \text{Percent [%]}=\frac{\text{# Ann. introns by splice site}}{\text{# Annotated introns}}*100\% \]
Reads - annotated introns
Cluster # Annotated introns # Reads in cluster # Ann. intron reads Percentage [%]
case 109950 120642911 73861148 61.22
control 109950 127058916 84110749 66.20
Expand details
  • # Annotated introns: number of common annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Ann. intron reads: reads associated to the annotated introns in the cluster. Only common introns are being counted.
  • Percent [%]: the percentage that the annotated intron reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Ann. intron reads}}{\text{# Reads in cluster}}*100\% \]
Reads - novel junctions
Cluster Novel type # Novel junctions # Novel junc. in splice site # Reads in cluster # Novel junc. reads Percentage [%]
case novel_acceptor 71101 40621 120642911 150627 0.12
case novel_donor 71101 30480 120642911 116941 0.10
control novel_acceptor 56579 32499 127058916 127074 0.10
control novel_donor 56579 24080 127058916 98371 0.08
Expand details
  • # Novel junctions: total number of novel junctions for that particular cluster.
  • # Novel junc. in splice site: total number of novel junctions for that particular splice site in the cluster.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Novel junc. reads: reads associated to the novel junctions in the cluster and splice site.
  • Percent [%]: the percentage that the novel junction reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Novel junc. reads}}{\text{# Reads in cluster}}*100\% \]

3.2 Spliceosome

AQR

ENCODE experiment summary:

Click for details

Information:

  • Target: AQR
  • Category: Spliceosome
  • Assay: shRNA knockdown followed by RNA-seq
  • Nucleic acid type: polyadenylated mRNA
  • Lab: Brenton Gravely, UConn

Samples analysed:

  • 4 case samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 9.2 [1-1], 9.4 [2-1]
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 9.2
  • 4 control samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 9.6 [2-1], 10.0 [1-1]
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 9.7 [1-1], 9.2 [2-1]

Distances (N)

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions. Bars are stacked.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and cluster (same as colour).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Difference between the number of unique novel junctions from case samples and from control samples.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Modulo 3

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Number of unique novel junctions. Also represented as the text inside the bars.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control) and novel type (donor and acceptor).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control), novel type (donor and acceptor) and sequence (intronic and exonic).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and sequence (intronic vs. exonic).

Delta MaxEntScan

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Kernel density estimate (smoothed version of a histogram).
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Difference between the kernel density estimate for case samples and control samples.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

MSR

Expand details
  • X-Axis: The mis-splicing ratio.
  • Y-Axis: Kernel density estimate.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.
  • Notes: Distributions have a discontinuity at X = 0.05 to better represent all possible MSR values. In some cases, a discontinuity in the Y-axis is also present if the difference between the two sample types exceeds a predefined threshold.

Stats

Unique annotated introns
Mis-spliced site Cluster # Annotated introns # Ann. introns by splice site Percent [%]
acceptor case 109950 36429 33.13
acceptor control 109950 18224 16.57
both case 109950 34316 31.21
both control 109950 10856 9.87
donor case 109950 7396 6.73
donor control 109950 11068 10.07
never case 109950 31809 28.93
never control 109950 69802 63.49
Expand details
  • # Annotated introns: number of total annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Ann. introns by splice site: the number of annotated introns for the cluster and splice site.
  • Percent [%]: the percentage that the annotated introns in the splice site represent to the total number of introns in the cluster:
\[ \text{Percent [%]}=\frac{\text{# Ann. introns by splice site}}{\text{# Annotated introns}}*100\% \]
Reads - annotated introns
Cluster # Annotated introns # Reads in cluster # Ann. intron reads Percentage [%]
case 109950 133197366 70652393 53.04
control 109950 126533708 81822502 64.66
Expand details
  • # Annotated introns: number of common annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Ann. intron reads: reads associated to the annotated introns in the cluster. Only common introns are being counted.
  • Percent [%]: the percentage that the annotated intron reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Ann. intron reads}}{\text{# Reads in cluster}}*100\% \]
Reads - novel junctions
Cluster Novel type # Novel junctions # Novel junc. in splice site # Reads in cluster # Novel junc. reads Percentage [%]
case novel_acceptor 289498 216314 133197366 995257 0.75
case novel_donor 289498 73184 133197366 260535 0.20
control novel_acceptor 71583 40904 126533708 158410 0.13
control novel_donor 71583 30679 126533708 122555 0.10
Expand details
  • # Novel junctions: total number of novel junctions for that particular cluster.
  • # Novel junc. in splice site: total number of novel junctions for that particular splice site in the cluster.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Novel junc. reads: reads associated to the novel junctions in the cluster and splice site.
  • Percent [%]: the percentage that the novel junction reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Novel junc. reads}}{\text{# Reads in cluster}}*100\% \]

SF3A3

ENCODE experiment summary:

Click for details

Information:

  • Target: SF3A3
  • Category: Spliceosome
  • Assay: shRNA knockdown followed by RNA-seq
  • Nucleic acid type: polyadenylated mRNA
  • Lab: Brenton Gravely, UConn

Samples analysed:

  • 4 case samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 9.8 [1-1], 10.0 [2-1]
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 10
  • 4 control samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 10
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 10

Distances (N)

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions. Bars are stacked.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and cluster (same as colour).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Difference between the number of unique novel junctions from case samples and from control samples.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Modulo 3

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Number of unique novel junctions. Also represented as the text inside the bars.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control) and novel type (donor and acceptor).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control), novel type (donor and acceptor) and sequence (intronic and exonic).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and sequence (intronic vs. exonic).

Delta MaxEntScan

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Kernel density estimate (smoothed version of a histogram).
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Difference between the kernel density estimate for case samples and control samples.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

MSR

Expand details
  • X-Axis: The mis-splicing ratio.
  • Y-Axis: Kernel density estimate.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.
  • Notes: Distributions have a discontinuity at X = 0.05 to better represent all possible MSR values. In some cases, a discontinuity in the Y-axis is also present if the difference between the two sample types exceeds a predefined threshold.

Stats

Unique annotated introns
Mis-spliced site Cluster # Annotated introns # Ann. introns by splice site Percent [%]
acceptor case 109950 27909 25.38
acceptor control 109950 18108 16.47
both case 109950 16837 15.31
both control 109950 9740 8.86
donor case 109950 11808 10.74
donor control 109950 10428 9.48
never case 109950 53396 48.56
never control 109950 71674 65.19
Expand details
  • # Annotated introns: number of total annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Ann. introns by splice site: the number of annotated introns for the cluster and splice site.
  • Percent [%]: the percentage that the annotated introns in the splice site represent to the total number of introns in the cluster:
\[ \text{Percent [%]}=\frac{\text{# Ann. introns by splice site}}{\text{# Annotated introns}}*100\% \]
Reads - annotated introns
Cluster # Annotated introns # Reads in cluster # Ann. intron reads Percentage [%]
case 109950 171167876 91151237 53.25
control 109950 140949277 83680600 59.37
Expand details
  • # Annotated introns: number of common annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Ann. intron reads: reads associated to the annotated introns in the cluster. Only common introns are being counted.
  • Percent [%]: the percentage that the annotated intron reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Ann. intron reads}}{\text{# Reads in cluster}}*100\% \]
Reads - novel junctions
Cluster Novel type # Novel junctions # Novel junc. in splice site # Reads in cluster # Novel junc. reads Percentage [%]
case novel_acceptor 112924 71882 171167876 264601 0.15
case novel_donor 112924 41042 171167876 166485 0.10
control novel_acceptor 66349 38262 140949277 158158 0.11
control novel_donor 66349 28087 140949277 116118 0.08
Expand details
  • # Novel junctions: total number of novel junctions for that particular cluster.
  • # Novel junc. in splice site: total number of novel junctions for that particular splice site in the cluster.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Novel junc. reads: reads associated to the novel junctions in the cluster and splice site.
  • Percent [%]: the percentage that the novel junction reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Novel junc. reads}}{\text{# Reads in cluster}}*100\% \]

SF3B4

ENCODE experiment summary:

Click for details

Information:

  • Target: SF3B4
  • Category: Spliceosome
  • Assay: shRNA knockdown followed by RNA-seq
  • Nucleic acid type: polyadenylated mRNA
  • Lab: Brenton Gravely, UConn

Samples analysed:

  • 4 case samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 9.4 [2-1], 9.6 [1-1]
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 8.8 [1-1], 9.1 [2-1]
  • 4 control samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 9.5
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 9.2

Distances (N)

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions. Bars are stacked.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and cluster (same as colour).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Difference between the number of unique novel junctions from case samples and from control samples.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Modulo 3

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Number of unique novel junctions. Also represented as the text inside the bars.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control) and novel type (donor and acceptor).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control), novel type (donor and acceptor) and sequence (intronic and exonic).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and sequence (intronic vs. exonic).

Delta MaxEntScan

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Kernel density estimate (smoothed version of a histogram).
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Difference between the kernel density estimate for case samples and control samples.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

MSR

Expand details
  • X-Axis: The mis-splicing ratio.
  • Y-Axis: Kernel density estimate.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.
  • Notes: Distributions have a discontinuity at X = 0.05 to better represent all possible MSR values. In some cases, a discontinuity in the Y-axis is also present if the difference between the two sample types exceeds a predefined threshold.

Stats

Unique annotated introns
Mis-spliced site Cluster # Annotated introns # Ann. introns by splice site Percent [%]
acceptor case 109950 22865 20.80
acceptor control 109950 15927 14.49
both case 109950 10591 9.63
both control 109950 7631 6.94
donor case 109950 10165 9.25
donor control 109950 9453 8.60
never case 109950 66329 60.33
never control 109950 76939 69.98
Expand details
  • # Annotated introns: number of total annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Ann. introns by splice site: the number of annotated introns for the cluster and splice site.
  • Percent [%]: the percentage that the annotated introns in the splice site represent to the total number of introns in the cluster:
\[ \text{Percent [%]}=\frac{\text{# Ann. introns by splice site}}{\text{# Annotated introns}}*100\% \]
Reads - annotated introns
Cluster # Annotated introns # Reads in cluster # Ann. intron reads Percentage [%]
case 109950 112510049 64700999 57.51
control 109950 122011801 81627934 66.90
Expand details
  • # Annotated introns: number of common annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Ann. intron reads: reads associated to the annotated introns in the cluster. Only common introns are being counted.
  • Percent [%]: the percentage that the annotated intron reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Ann. intron reads}}{\text{# Reads in cluster}}*100\% \]
Reads - novel junctions
Cluster Novel type # Novel junctions # Novel junc. in splice site # Reads in cluster # Novel junc. reads Percentage [%]
case novel_acceptor 75020 47078 112510049 169880 0.15
case novel_donor 75020 27942 112510049 100554 0.09
control novel_acceptor 54596 31594 122011801 119731 0.10
control novel_donor 54596 23002 122011801 90714 0.07
Expand details
  • # Novel junctions: total number of novel junctions for that particular cluster.
  • # Novel junc. in splice site: total number of novel junctions for that particular splice site in the cluster.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Novel junc. reads: reads associated to the novel junctions in the cluster and splice site.
  • Percent [%]: the percentage that the novel junction reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Novel junc. reads}}{\text{# Reads in cluster}}*100\% \]

SNRNP200

ENCODE experiment summary:

Click for details

Information:

  • Target: SNRNP200
  • Category: Spliceosome
  • Assay: shRNA knockdown followed by RNA-seq
  • Nucleic acid type: polyadenylated mRNA
  • Lab: Brenton Gravely, UConn

Samples analysed:

  • 4 case samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 9.9
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 9.5 [1-1], 9.7 [2-1]
  • 4 control samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 9.7 [1-1], 9.8 [2-1]
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 10

Distances (N)

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions. Bars are stacked.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and cluster (same as colour).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Difference between the number of unique novel junctions from case samples and from control samples.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Modulo 3

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Number of unique novel junctions. Also represented as the text inside the bars.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control) and novel type (donor and acceptor).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control), novel type (donor and acceptor) and sequence (intronic and exonic).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and sequence (intronic vs. exonic).

Delta MaxEntScan

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Kernel density estimate (smoothed version of a histogram).
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Difference between the kernel density estimate for case samples and control samples.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

MSR

Expand details
  • X-Axis: The mis-splicing ratio.
  • Y-Axis: Kernel density estimate.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.
  • Notes: Distributions have a discontinuity at X = 0.05 to better represent all possible MSR values. In some cases, a discontinuity in the Y-axis is also present if the difference between the two sample types exceeds a predefined threshold.

Stats

Unique annotated introns
Mis-spliced site Cluster # Annotated introns # Ann. introns by splice site Percent [%]
acceptor case 109950 17301 15.74
acceptor control 109950 14640 13.32
both case 109950 9738 8.86
both control 109950 6722 6.11
donor case 109950 11024 10.03
donor control 109950 9241 8.40
never case 109950 71887 65.38
never control 109950 79347 72.17
Expand details
  • # Annotated introns: number of total annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Ann. introns by splice site: the number of annotated introns for the cluster and splice site.
  • Percent [%]: the percentage that the annotated introns in the splice site represent to the total number of introns in the cluster:
\[ \text{Percent [%]}=\frac{\text{# Ann. introns by splice site}}{\text{# Annotated introns}}*100\% \]
Reads - annotated introns
Cluster # Annotated introns # Reads in cluster # Ann. intron reads Percentage [%]
case 109950 134926056 71707770 53.15
control 109950 130648179 82068661 62.82
Expand details
  • # Annotated introns: number of common annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Ann. intron reads: reads associated to the annotated introns in the cluster. Only common introns are being counted.
  • Percent [%]: the percentage that the annotated intron reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Ann. intron reads}}{\text{# Reads in cluster}}*100\% \]
Reads - novel junctions
Cluster Novel type # Novel junctions # Novel junc. in splice site # Reads in cluster # Novel junc. reads Percentage [%]
case novel_acceptor 65685 37169 134926056 152506 0.11
case novel_donor 65685 28516 134926056 113426 0.08
control novel_acceptor 48974 27806 130648179 146489 0.11
control novel_donor 48974 21168 130648179 107454 0.08
Expand details
  • # Novel junctions: total number of novel junctions for that particular cluster.
  • # Novel junc. in splice site: total number of novel junctions for that particular splice site in the cluster.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Novel junc. reads: reads associated to the novel junctions in the cluster and splice site.
  • Percent [%]: the percentage that the novel junction reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Novel junc. reads}}{\text{# Reads in cluster}}*100\% \]

PRPF4

ENCODE experiment summary:

Click for details

Information:

  • Target: PRPF4
  • Category: Spliceosome
  • Assay: shRNA knockdown followed by RNA-seq
  • Nucleic acid type: polyadenylated mRNA
  • Lab: Brenton Gravely, UConn

Samples analysed:

  • 4 case samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 9.8 [1-1], 10.0 [2-1]
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 8.8 [1-1], 8.9 [2-1]
  • 4 control samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 10.0 [1-1], 9.6 [2-1]
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 9.2 [2-1], 9.7 [1-1]

Distances (N)

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions. Bars are stacked.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and cluster (same as colour).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Difference between the number of unique novel junctions from case samples and from control samples.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Modulo 3

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Number of unique novel junctions. Also represented as the text inside the bars.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control) and novel type (donor and acceptor).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control), novel type (donor and acceptor) and sequence (intronic and exonic).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and sequence (intronic vs. exonic).

Delta MaxEntScan

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Kernel density estimate (smoothed version of a histogram).
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Difference between the kernel density estimate for case samples and control samples.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

MSR

Expand details
  • X-Axis: The mis-splicing ratio.
  • Y-Axis: Kernel density estimate.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.
  • Notes: Distributions have a discontinuity at X = 0.05 to better represent all possible MSR values. In some cases, a discontinuity in the Y-axis is also present if the difference between the two sample types exceeds a predefined threshold.

Stats

Unique annotated introns
Mis-spliced site Cluster # Annotated introns # Ann. introns by splice site Percent [%]
acceptor case 109950 15878 14.44
acceptor control 109950 13582 12.35
both case 109950 7066 6.43
both control 109950 5955 5.42
donor case 109950 9781 8.90
donor control 109950 8757 7.96
never case 109950 77225 70.24
never control 109950 81656 74.27
Expand details
  • # Annotated introns: number of total annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Ann. introns by splice site: the number of annotated introns for the cluster and splice site.
  • Percent [%]: the percentage that the annotated introns in the splice site represent to the total number of introns in the cluster:
\[ \text{Percent [%]}=\frac{\text{# Ann. introns by splice site}}{\text{# Annotated introns}}*100\% \]
Reads - annotated introns
Cluster # Annotated introns # Reads in cluster # Ann. intron reads Percentage [%]
case 109950 80269690 46414907 57.82
control 109950 71066567 42863013 60.31
Expand details
  • # Annotated introns: number of common annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Ann. intron reads: reads associated to the annotated introns in the cluster. Only common introns are being counted.
  • Percent [%]: the percentage that the annotated intron reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Ann. intron reads}}{\text{# Reads in cluster}}*100\% \]
Reads - novel junctions
Cluster Novel type # Novel junctions # Novel junc. in splice site # Reads in cluster # Novel junc. reads Percentage [%]
case novel_acceptor 52297 30224 80269690 93808 0.12
case novel_donor 52297 22073 80269690 72979 0.09
control novel_acceptor 43798 24870 71066567 80646 0.11
control novel_donor 43798 18928 71066567 62007 0.09
Expand details
  • # Novel junctions: total number of novel junctions for that particular cluster.
  • # Novel junc. in splice site: total number of novel junctions for that particular splice site in the cluster.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Novel junc. reads: reads associated to the novel junctions in the cluster and splice site.
  • Percent [%]: the percentage that the novel junction reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Novel junc. reads}}{\text{# Reads in cluster}}*100\% \]

SART3

ENCODE experiment summary:

Click for details

Information:

  • Target: SART3
  • Category: Spliceosome
  • Assay: shRNA knockdown followed by RNA-seq
  • Nucleic acid type: polyadenylated mRNA
  • Lab: Brenton Gravely, UConn

Samples analysed:

  • 4 case samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 9.5 [1-1], 9.8 [2-1]
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 8.6 [1-1], 9.4 [2-1]
  • 4 control samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 9.8 [1-1], 9.9 [2-1]
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 9.7 [1-1], 9.8 [2-1]

Distances (N)

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions. Bars are stacked.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and cluster (same as colour).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Difference between the number of unique novel junctions from case samples and from control samples.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Modulo 3

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Number of unique novel junctions. Also represented as the text inside the bars.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control) and novel type (donor and acceptor).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control), novel type (donor and acceptor) and sequence (intronic and exonic).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and sequence (intronic vs. exonic).

Delta MaxEntScan

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Kernel density estimate (smoothed version of a histogram).
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Difference between the kernel density estimate for case samples and control samples.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

MSR

Expand details
  • X-Axis: The mis-splicing ratio.
  • Y-Axis: Kernel density estimate.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.
  • Notes: Distributions have a discontinuity at X = 0.05 to better represent all possible MSR values. In some cases, a discontinuity in the Y-axis is also present if the difference between the two sample types exceeds a predefined threshold.

Stats

Unique annotated introns
Mis-spliced site Cluster # Annotated introns # Ann. introns by splice site Percent [%]
acceptor case 109950 17607 16.01
acceptor control 109950 16315 14.84
both case 109950 9198 8.37
both control 109950 8259 7.51
donor case 109950 10187 9.27
donor control 109950 9547 8.68
never case 109950 72958 66.36
never control 109950 75829 68.97
Expand details
  • # Annotated introns: number of total annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Ann. introns by splice site: the number of annotated introns for the cluster and splice site.
  • Percent [%]: the percentage that the annotated introns in the splice site represent to the total number of introns in the cluster:
\[ \text{Percent [%]}=\frac{\text{# Ann. introns by splice site}}{\text{# Annotated introns}}*100\% \]
Reads - annotated introns
Cluster # Annotated introns # Reads in cluster # Ann. intron reads Percentage [%]
case 109950 151041133 86623869 57.35
control 109950 123467051 73104575 59.21
Expand details
  • # Annotated introns: number of common annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Ann. intron reads: reads associated to the annotated introns in the cluster. Only common introns are being counted.
  • Percent [%]: the percentage that the annotated intron reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Ann. intron reads}}{\text{# Reads in cluster}}*100\% \]
Reads - novel junctions
Cluster Novel type # Novel junctions # Novel junc. in splice site # Reads in cluster # Novel junc. reads Percentage [%]
case novel_acceptor 62842 36443 151041133 172136 0.11
case novel_donor 62842 26399 151041133 127177 0.08
control novel_acceptor 56647 32910 123467051 143879 0.12
control novel_donor 56647 23737 123467051 103935 0.08
Expand details
  • # Novel junctions: total number of novel junctions for that particular cluster.
  • # Novel junc. in splice site: total number of novel junctions for that particular splice site in the cluster.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Novel junc. reads: reads associated to the novel junctions in the cluster and splice site.
  • Percent [%]: the percentage that the novel junction reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Novel junc. reads}}{\text{# Reads in cluster}}*100\% \]

SMNDC1

ENCODE experiment summary:

Click for details

Information:

  • Target: SMNDC1
  • Category: Spliceosome
  • Assay: shRNA knockdown followed by RNA-seq
  • Nucleic acid type: polyadenylated mRNA
  • Lab: Brenton Gravely, UConn

Samples analysed:

  • 4 case samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 9.5 [1-1], 9.6 [2-1]
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 9.3
  • 4 control samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 9.4 [1-1], 9.5 [2-1]
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 9.5 [1-1], 9.3 [2-1]

Distances (N)

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions. Bars are stacked.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and cluster (same as colour).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Difference between the number of unique novel junctions from case samples and from control samples.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Modulo 3

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Number of unique novel junctions. Also represented as the text inside the bars.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control) and novel type (donor and acceptor).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control), novel type (donor and acceptor) and sequence (intronic and exonic).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and sequence (intronic vs. exonic).

Delta MaxEntScan

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Kernel density estimate (smoothed version of a histogram).
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Difference between the kernel density estimate for case samples and control samples.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

MSR

Expand details
  • X-Axis: The mis-splicing ratio.
  • Y-Axis: Kernel density estimate.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.
  • Notes: Distributions have a discontinuity at X = 0.05 to better represent all possible MSR values. In some cases, a discontinuity in the Y-axis is also present if the difference between the two sample types exceeds a predefined threshold.

Stats

Unique annotated introns
Mis-spliced site Cluster # Annotated introns # Ann. introns by splice site Percent [%]
acceptor case 109950 16979 15.44
acceptor control 109950 16478 14.99
both case 109950 8517 7.75
both control 109950 8585 7.81
donor case 109950 9971 9.07
donor control 109950 10050 9.14
never case 109950 74483 67.74
never control 109950 74837 68.06
Expand details
  • # Annotated introns: number of total annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Ann. introns by splice site: the number of annotated introns for the cluster and splice site.
  • Percent [%]: the percentage that the annotated introns in the splice site represent to the total number of introns in the cluster:
\[ \text{Percent [%]}=\frac{\text{# Ann. introns by splice site}}{\text{# Annotated introns}}*100\% \]
Reads - annotated introns
Cluster # Annotated introns # Reads in cluster # Ann. intron reads Percentage [%]
case 109950 97561814 62255240 63.81
control 109950 95867805 61574898 64.23
Expand details
  • # Annotated introns: number of common annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Ann. intron reads: reads associated to the annotated introns in the cluster. Only common introns are being counted.
  • Percent [%]: the percentage that the annotated intron reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Ann. intron reads}}{\text{# Reads in cluster}}*100\% \]
Reads - novel junctions
Cluster Novel type # Novel junctions # Novel junc. in splice site # Reads in cluster # Novel junc. reads Percentage [%]
case novel_acceptor 59168 34294 97561814 119422 0.12
case novel_donor 59168 24874 97561814 86686 0.09
control novel_acceptor 58648 33384 95867805 114395 0.12
control novel_donor 58648 25264 95867805 86835 0.09
Expand details
  • # Novel junctions: total number of novel junctions for that particular cluster.
  • # Novel junc. in splice site: total number of novel junctions for that particular splice site in the cluster.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Novel junc. reads: reads associated to the novel junctions in the cluster and splice site.
  • Percent [%]: the percentage that the novel junction reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Novel junc. reads}}{\text{# Reads in cluster}}*100\% \]

3.3 Nononsense-mediated decay

PABPC1

ENCODE experiment summary:

Click for details

Information:

  • Target: PABPC1
  • Category: NMD
  • Assay: shRNA knockdown followed by RNA-seq
  • Nucleic acid type: polyadenylated mRNA
  • Lab: Brenton Gravely, UConn

Samples analysed:

  • 4 case samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 9.9
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 9.9 [1-1], 9.8 [2-1]
  • 4 control samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 9.8 [1-1], 9.9 [2-1]
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 9.7 [1-1], 9.8 [2-1]

Distances (N)

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions. Bars are stacked.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and cluster (same as colour).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Difference between the number of unique novel junctions from case samples and from control samples.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Modulo 3

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Number of unique novel junctions. Also represented as the text inside the bars.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control) and novel type (donor and acceptor).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control), novel type (donor and acceptor) and sequence (intronic and exonic).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and sequence (intronic vs. exonic).

Delta MaxEntScan

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Kernel density estimate (smoothed version of a histogram).
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Difference between the kernel density estimate for case samples and control samples.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

MSR

Expand details
  • X-Axis: The mis-splicing ratio.
  • Y-Axis: Kernel density estimate.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.
  • Notes: Distributions have a discontinuity at X = 0.05 to better represent all possible MSR values. In some cases, a discontinuity in the Y-axis is also present if the difference between the two sample types exceeds a predefined threshold.

Stats

Unique annotated introns
Mis-spliced site Cluster # Annotated introns # Ann. introns by splice site Percent [%]
acceptor case 109950 20302 18.46
acceptor control 109950 16315 14.84
both case 109950 11993 10.91
both control 109950 8259 7.51
donor case 109950 10718 9.75
donor control 109950 9547 8.68
never case 109950 66937 60.88
never control 109950 75829 68.97
Expand details
  • # Annotated introns: number of total annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Ann. introns by splice site: the number of annotated introns for the cluster and splice site.
  • Percent [%]: the percentage that the annotated introns in the splice site represent to the total number of introns in the cluster:
\[ \text{Percent [%]}=\frac{\text{# Ann. introns by splice site}}{\text{# Annotated introns}}*100\% \]
Reads - annotated introns
Cluster # Annotated introns # Reads in cluster # Ann. intron reads Percentage [%]
case 109950 148180187 79615414 53.73
control 109950 123467051 73104575 59.21
Expand details
  • # Annotated introns: number of common annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Ann. intron reads: reads associated to the annotated introns in the cluster. Only common introns are being counted.
  • Percent [%]: the percentage that the annotated intron reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Ann. intron reads}}{\text{# Reads in cluster}}*100\% \]
Reads - novel junctions
Cluster Novel type # Novel junctions # Novel junc. in splice site # Reads in cluster # Novel junc. reads Percentage [%]
case novel_acceptor 78549 46737 148180187 203284 0.14
case novel_donor 78549 31812 148180187 146294 0.10
control novel_acceptor 56647 32910 123467051 143879 0.12
control novel_donor 56647 23737 123467051 103935 0.08
Expand details
  • # Novel junctions: total number of novel junctions for that particular cluster.
  • # Novel junc. in splice site: total number of novel junctions for that particular splice site in the cluster.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Novel junc. reads: reads associated to the novel junctions in the cluster and splice site.
  • Percent [%]: the percentage that the novel junction reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Novel junc. reads}}{\text{# Reads in cluster}}*100\% \]

RPS19

ENCODE experiment summary:

Click for details

Information:

  • Target: RPS19
  • Category: NMD
  • Assay: shRNA knockdown followed by RNA-seq
  • Nucleic acid type: polyadenylated mRNA
  • Lab: Brenton Gravely, UConn

Samples analysed:

  • 4 case samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 9.2 [2-1], 9.1 [1-1]
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 8.7 [1-1], 8.8 [2-1]
  • 4 control samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 9.6
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 9.7 [1-1], 9.3 [2-1]

Distances (N)

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions. Bars are stacked.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and cluster (same as colour).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Difference between the number of unique novel junctions from case samples and from control samples.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Modulo 3

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Number of unique novel junctions. Also represented as the text inside the bars.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control) and novel type (donor and acceptor).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control), novel type (donor and acceptor) and sequence (intronic and exonic).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and sequence (intronic vs. exonic).

Delta MaxEntScan

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Kernel density estimate (smoothed version of a histogram).
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Difference between the kernel density estimate for case samples and control samples.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

MSR

Expand details
  • X-Axis: The mis-splicing ratio.
  • Y-Axis: Kernel density estimate.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.
  • Notes: Distributions have a discontinuity at X = 0.05 to better represent all possible MSR values. In some cases, a discontinuity in the Y-axis is also present if the difference between the two sample types exceeds a predefined threshold.

Stats

Unique annotated introns
Mis-spliced site Cluster # Annotated introns # Ann. introns by splice site Percent [%]
acceptor case 109950 16566 15.07
acceptor control 109950 14086 12.81
both case 109950 8810 8.01
both control 109950 6434 5.85
donor case 109950 10964 9.97
donor control 109950 8886 8.08
never case 109950 73610 66.95
never control 109950 80544 73.26
Expand details
  • # Annotated introns: number of total annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Ann. introns by splice site: the number of annotated introns for the cluster and splice site.
  • Percent [%]: the percentage that the annotated introns in the splice site represent to the total number of introns in the cluster:
\[ \text{Percent [%]}=\frac{\text{# Ann. introns by splice site}}{\text{# Annotated introns}}*100\% \]
Reads - annotated introns
Cluster # Annotated introns # Reads in cluster # Ann. intron reads Percentage [%]
case 109950 80807406 49789650 61.62
control 109950 65858978 42355364 64.31
Expand details
  • # Annotated introns: number of common annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Ann. intron reads: reads associated to the annotated introns in the cluster. Only common introns are being counted.
  • Percent [%]: the percentage that the annotated intron reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Ann. intron reads}}{\text{# Reads in cluster}}*100\% \]
Reads - novel junctions
Cluster Novel type # Novel junctions # Novel junc. in splice site # Reads in cluster # Novel junc. reads Percentage [%]
case novel_acceptor 60820 33896 80807406 111289 0.14
case novel_donor 60820 26924 80807406 87885 0.11
control novel_acceptor 45976 26222 65858978 79648 0.12
control novel_donor 45976 19754 65858978 59477 0.09
Expand details
  • # Novel junctions: total number of novel junctions for that particular cluster.
  • # Novel junc. in splice site: total number of novel junctions for that particular splice site in the cluster.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Novel junc. reads: reads associated to the novel junctions in the cluster and splice site.
  • Percent [%]: the percentage that the novel junction reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Novel junc. reads}}{\text{# Reads in cluster}}*100\% \]

RPS3A

ENCODE experiment summary:

Click for details

Information:

  • Target: RPS3A
  • Category: NMD
  • Assay: shRNA knockdown followed by RNA-seq
  • Nucleic acid type: polyadenylated mRNA
  • Lab: Brenton Gravely, UConn

Samples analysed:

  • 4 case samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 9.6 [2-1], 9.1 [1-1]
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 9.5 [1-1], 9.4 [2-1]
  • 4 control samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 9.8 [1-1], 9.9 [2-1]
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 9.7 [1-1], 9.8 [2-1]

Distances (N)

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions. Bars are stacked.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and cluster (same as colour).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Difference between the number of unique novel junctions from case samples and from control samples.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Modulo 3

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Number of unique novel junctions. Also represented as the text inside the bars.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control) and novel type (donor and acceptor).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control), novel type (donor and acceptor) and sequence (intronic and exonic).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and sequence (intronic vs. exonic).

Delta MaxEntScan

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Kernel density estimate (smoothed version of a histogram).
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Difference between the kernel density estimate for case samples and control samples.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

MSR

Expand details
  • X-Axis: The mis-splicing ratio.
  • Y-Axis: Kernel density estimate.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.
  • Notes: Distributions have a discontinuity at X = 0.05 to better represent all possible MSR values. In some cases, a discontinuity in the Y-axis is also present if the difference between the two sample types exceeds a predefined threshold.

Stats

Unique annotated introns
Mis-spliced site Cluster # Annotated introns # Ann. introns by splice site Percent [%]
acceptor case 109950 17538 15.95
acceptor control 109950 16315 14.84
both case 109950 9245 8.41
both control 109950 8259 7.51
donor case 109950 10300 9.37
donor control 109950 9547 8.68
never case 109950 72867 66.27
never control 109950 75829 68.97
Expand details
  • # Annotated introns: number of total annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Ann. introns by splice site: the number of annotated introns for the cluster and splice site.
  • Percent [%]: the percentage that the annotated introns in the splice site represent to the total number of introns in the cluster:
\[ \text{Percent [%]}=\frac{\text{# Ann. introns by splice site}}{\text{# Annotated introns}}*100\% \]
Reads - annotated introns
Cluster # Annotated introns # Reads in cluster # Ann. intron reads Percentage [%]
case 109950 135803280 77474141 57.05
control 109950 123467051 73104575 59.21
Expand details
  • # Annotated introns: number of common annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Ann. intron reads: reads associated to the annotated introns in the cluster. Only common introns are being counted.
  • Percent [%]: the percentage that the annotated intron reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Ann. intron reads}}{\text{# Reads in cluster}}*100\% \]
Reads - novel junctions
Cluster Novel type # Novel junctions # Novel junc. in splice site # Reads in cluster # Novel junc. reads Percentage [%]
case novel_acceptor 62783 36110 135803280 152543 0.11
case novel_donor 62783 26673 135803280 111983 0.08
control novel_acceptor 56647 32910 123467051 143879 0.12
control novel_donor 56647 23737 123467051 103935 0.08
Expand details
  • # Novel junctions: total number of novel junctions for that particular cluster.
  • # Novel junc. in splice site: total number of novel junctions for that particular splice site in the cluster.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Novel junc. reads: reads associated to the novel junctions in the cluster and splice site.
  • Percent [%]: the percentage that the novel junction reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Novel junc. reads}}{\text{# Reads in cluster}}*100\% \]

RPS10

ENCODE experiment summary:

Click for details

Information:

  • Target: RPS10
  • Category: NMD
  • Assay: shRNA knockdown followed by RNA-seq
  • Nucleic acid type: polyadenylated mRNA
  • Lab: Brenton Gravely, UConn

Samples analysed:

  • 4 case samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 9.4
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 9.3 [1-1], 9.2 [2-1]
  • 4 control samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 9.4 [1-1], 9.5 [2-1]
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 9.4 [1-1], 9.3 [2-1]

Distances (N)

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions. Bars are stacked.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and cluster (same as colour).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Difference between the number of unique novel junctions from case samples and from control samples.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Modulo 3

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Number of unique novel junctions. Also represented as the text inside the bars.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control) and novel type (donor and acceptor).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control), novel type (donor and acceptor) and sequence (intronic and exonic).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and sequence (intronic vs. exonic).

Delta MaxEntScan

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Kernel density estimate (smoothed version of a histogram).
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Difference between the kernel density estimate for case samples and control samples.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

MSR

Expand details
  • X-Axis: The mis-splicing ratio.
  • Y-Axis: Kernel density estimate.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.
  • Notes: Distributions have a discontinuity at X = 0.05 to better represent all possible MSR values. In some cases, a discontinuity in the Y-axis is also present if the difference between the two sample types exceeds a predefined threshold.

Stats

Unique annotated introns
Mis-spliced site Cluster # Annotated introns # Ann. introns by splice site Percent [%]
acceptor case 109950 15632 14.22
acceptor control 109950 15541 14.13
both case 109950 7820 7.11
both control 109950 7891 7.18
donor case 109950 9761 8.88
donor control 109950 9775 8.89
never case 109950 76737 69.79
never control 109950 76743 69.80
Expand details
  • # Annotated introns: number of total annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Ann. introns by splice site: the number of annotated introns for the cluster and splice site.
  • Percent [%]: the percentage that the annotated introns in the splice site represent to the total number of introns in the cluster:
\[ \text{Percent [%]}=\frac{\text{# Ann. introns by splice site}}{\text{# Annotated introns}}*100\% \]
Reads - annotated introns
Cluster # Annotated introns # Reads in cluster # Ann. intron reads Percentage [%]
case 109950 87700972 55703851 63.52
control 109950 88157283 55672338 63.15
Expand details
  • # Annotated introns: number of common annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Ann. intron reads: reads associated to the annotated introns in the cluster. Only common introns are being counted.
  • Percent [%]: the percentage that the annotated intron reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Ann. intron reads}}{\text{# Reads in cluster}}*100\% \]
Reads - novel junctions
Cluster Novel type # Novel junctions # Novel junc. in splice site # Reads in cluster # Novel junc. reads Percentage [%]
case novel_acceptor 54326 30946 87700972 101282 0.12
case novel_donor 54326 23380 87700972 78126 0.09
control novel_acceptor 54588 30897 88157283 100494 0.11
control novel_donor 54588 23691 88157283 79025 0.09
Expand details
  • # Novel junctions: total number of novel junctions for that particular cluster.
  • # Novel junc. in splice site: total number of novel junctions for that particular splice site in the cluster.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Novel junc. reads: reads associated to the novel junctions in the cluster and splice site.
  • Percent [%]: the percentage that the novel junction reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Novel junc. reads}}{\text{# Reads in cluster}}*100\% \]

EIF4G1

ENCODE experiment summary:

Click for details

Information:

  • Target: EIF4G1
  • Category: NMD
  • Assay: shRNA knockdown followed by RNA-seq
  • Nucleic acid type: polyadenylated mRNA
  • Lab: Brenton Gravely, UConn

Samples analysed:

  • 4 case samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 9.7
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 9.7 [1-1], 9.6 [2-1]
  • 4 control samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 9.7 [1-1], 9.6 [2-1]
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 9.7 [1-1], 9.8 [2-1]

Distances (N)

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions. Bars are stacked.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and cluster (same as colour).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Difference between the number of unique novel junctions from case samples and from control samples.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Modulo 3

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Number of unique novel junctions. Also represented as the text inside the bars.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control) and novel type (donor and acceptor).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control), novel type (donor and acceptor) and sequence (intronic and exonic).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and sequence (intronic vs. exonic).

Delta MaxEntScan

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Kernel density estimate (smoothed version of a histogram).
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Difference between the kernel density estimate for case samples and control samples.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

MSR

Expand details
  • X-Axis: The mis-splicing ratio.
  • Y-Axis: Kernel density estimate.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.
  • Notes: Distributions have a discontinuity at X = 0.05 to better represent all possible MSR values. In some cases, a discontinuity in the Y-axis is also present if the difference between the two sample types exceeds a predefined threshold.

Stats

Unique annotated introns
Mis-spliced site Cluster # Annotated introns # Ann. introns by splice site Percent [%]
acceptor case 109950 16595 15.09
acceptor control 109950 16787 15.27
both case 109950 8051 7.32
both control 109950 8441 7.68
donor case 109950 9968 9.07
donor control 109950 9776 8.89
never case 109950 75336 68.52
never control 109950 74946 68.16
Expand details
  • # Annotated introns: number of total annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Ann. introns by splice site: the number of annotated introns for the cluster and splice site.
  • Percent [%]: the percentage that the annotated introns in the splice site represent to the total number of introns in the cluster:
\[ \text{Percent [%]}=\frac{\text{# Ann. introns by splice site}}{\text{# Annotated introns}}*100\% \]
Reads - annotated introns
Cluster # Annotated introns # Reads in cluster # Ann. intron reads Percentage [%]
case 109950 100953374 63435477 62.84
control 109950 110552729 70304787 63.59
Expand details
  • # Annotated introns: number of common annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Ann. intron reads: reads associated to the annotated introns in the cluster. Only common introns are being counted.
  • Percent [%]: the percentage that the annotated intron reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Ann. intron reads}}{\text{# Reads in cluster}}*100\% \]
Reads - novel junctions
Cluster Novel type # Novel junctions # Novel junc. in splice site # Reads in cluster # Novel junc. reads Percentage [%]
case novel_acceptor 56388 32491 100953374 113971 0.11
case novel_donor 56388 23897 100953374 84617 0.08
control novel_acceptor 58421 33887 110552729 123550 0.11
control novel_donor 58421 24534 110552729 90550 0.08
Expand details
  • # Novel junctions: total number of novel junctions for that particular cluster.
  • # Novel junc. in splice site: total number of novel junctions for that particular splice site in the cluster.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Novel junc. reads: reads associated to the novel junctions in the cluster and splice site.
  • Percent [%]: the percentage that the novel junction reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Novel junc. reads}}{\text{# Reads in cluster}}*100\% \]

3.4 Exon junction complex

EIF4A3

ENCODE experiment summary:

Click for details

Information:

  • Target: EIF4A3
  • Category: Exon_junction_complex
  • Assay: shRNA knockdown followed by RNA-seq
  • Nucleic acid type: polyadenylated mRNA
  • Lab: Brenton Gravely, UConn

Samples analysed:

  • 4 case samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 9.1 [1-1], 7.7 [2-1]
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 9.7 [1-1], 9.2 [2-1]
  • 4 control samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 8.9
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 9.2

Distances (N)

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions. Bars are stacked.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and cluster (same as colour).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Difference between the number of unique novel junctions from case samples and from control samples.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Modulo 3

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Number of unique novel junctions. Also represented as the text inside the bars.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control) and novel type (donor and acceptor).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control), novel type (donor and acceptor) and sequence (intronic and exonic).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and sequence (intronic vs. exonic).

Delta MaxEntScan

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Kernel density estimate (smoothed version of a histogram).
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Difference between the kernel density estimate for case samples and control samples.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

MSR

Expand details
  • X-Axis: The mis-splicing ratio.
  • Y-Axis: Kernel density estimate.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.
  • Notes: Distributions have a discontinuity at X = 0.05 to better represent all possible MSR values. In some cases, a discontinuity in the Y-axis is also present if the difference between the two sample types exceeds a predefined threshold.

Stats

Unique annotated introns
Mis-spliced site Cluster # Annotated introns # Ann. introns by splice site Percent [%]
acceptor case 109950 21429 19.49
acceptor control 109950 16352 14.87
both case 109950 14960 13.61
both control 109950 7395 6.73
donor case 109950 13449 12.23
donor control 109950 9541 8.68
never case 109950 60112 54.67
never control 109950 76662 69.72
Expand details
  • # Annotated introns: number of total annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Ann. introns by splice site: the number of annotated introns for the cluster and splice site.
  • Percent [%]: the percentage that the annotated introns in the splice site represent to the total number of introns in the cluster:
\[ \text{Percent [%]}=\frac{\text{# Ann. introns by splice site}}{\text{# Annotated introns}}*100\% \]
Reads - annotated introns
Cluster # Annotated introns # Reads in cluster # Ann. intron reads Percentage [%]
case 109950 114070552 72091127 63.20
control 109950 117220176 78940705 67.34
Expand details
  • # Annotated introns: number of common annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Ann. intron reads: reads associated to the annotated introns in the cluster. Only common introns are being counted.
  • Percent [%]: the percentage that the annotated intron reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Ann. intron reads}}{\text{# Reads in cluster}}*100\% \]
Reads - novel junctions
Cluster Novel type # Novel junctions # Novel junc. in splice site # Reads in cluster # Novel junc. reads Percentage [%]
case novel_acceptor 98532 56033 114070552 221927 0.19
case novel_donor 98532 42499 114070552 183352 0.16
control novel_acceptor 54022 31483 117220176 119271 0.10
control novel_donor 54022 22539 117220176 89354 0.08
Expand details
  • # Novel junctions: total number of novel junctions for that particular cluster.
  • # Novel junc. in splice site: total number of novel junctions for that particular splice site in the cluster.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Novel junc. reads: reads associated to the novel junctions in the cluster and splice site.
  • Percent [%]: the percentage that the novel junction reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Novel junc. reads}}{\text{# Reads in cluster}}*100\% \]

MAGOH

ENCODE experiment summary:

Click for details

Information:

  • Target: MAGOH
  • Category: Exon_junction_complex
  • Assay: shRNA knockdown followed by RNA-seq
  • Nucleic acid type: polyadenylated mRNA
  • Lab: Brenton Gravely, UConn

Samples analysed:

  • 4 case samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 9.4
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 9
  • 4 control samples:
    • 2 samples from HepG2 cell lines (child, 15), with 2 isogenic replicates; RIN 8.9
    • 2 samples from K562 cell lines (adult, 53), with 2 isogenic replicates; RIN 9.0 [1-1], 9.2 [2-1]

Distances (N)

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions. Bars are stacked.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Number of unique novel junctions.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and cluster (same as colour).

Expand details
  • X-Axis: Distance between the novel splice site and the reference splice site.
  • Y-Axis: Difference between the number of unique novel junctions from case samples and from control samples.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Modulo 3

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Number of unique novel junctions. Also represented as the text inside the bars.
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control) and novel type (donor and acceptor).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor).

Expand details
  • X-Axis: Distance in modulo 3 between the novel splice site and the reference splice site. Filtered by \(distance\leq 100\;bp\).
  • Y-Axis: Percentage of each modulo 3 value with respect to cluster (case and control), novel type (donor and acceptor) and sequence (intronic and exonic).
  • Colour: Cluster type as case vs. control.
  • Facets: Novel junction category (Novel donor vs. Novel acceptor) and sequence (intronic vs. exonic).

Delta MaxEntScan

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Kernel density estimate (smoothed version of a histogram).
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

Expand details
  • X-Axis: Difference between the MaxEntScan score of the reference annotated intron and the novel junction.
  • Y-Axis: Difference between the kernel density estimate for case samples and control samples.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.

MSR

Expand details
  • X-Axis: The mis-splicing ratio.
  • Y-Axis: Kernel density estimate.
  • Colour: Cluster type as case vs. control.
  • Facets: Different splice sites.
  • Notes: Distributions have a discontinuity at X = 0.05 to better represent all possible MSR values. In some cases, a discontinuity in the Y-axis is also present if the difference between the two sample types exceeds a predefined threshold.

Stats

Unique annotated introns
Mis-spliced site Cluster # Annotated introns # Ann. introns by splice site Percent [%]
acceptor case 109950 22677 20.62
acceptor control 109950 16339 14.86
both case 109950 14993 13.64
both control 109950 7938 7.22
donor case 109950 12787 11.63
donor control 109950 9806 8.92
never case 109950 59493 54.11
never control 109950 75867 69.00
Expand details
  • # Annotated introns: number of total annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Ann. introns by splice site: the number of annotated introns for the cluster and splice site.
  • Percent [%]: the percentage that the annotated introns in the splice site represent to the total number of introns in the cluster:
\[ \text{Percent [%]}=\frac{\text{# Ann. introns by splice site}}{\text{# Annotated introns}}*100\% \]
Reads - annotated introns
Cluster # Annotated introns # Reads in cluster # Ann. intron reads Percentage [%]
case 109950 121889488 75178667 61.68
control 109950 127058916 84110749 66.20
Expand details
  • # Annotated introns: number of common annotated introns in the cluster. Since we limit the annotated introns to those common across all samples and clusters, the number is the same for both clusters.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Ann. intron reads: reads associated to the annotated introns in the cluster. Only common introns are being counted.
  • Percent [%]: the percentage that the annotated intron reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Ann. intron reads}}{\text{# Reads in cluster}}*100\% \]
Reads - novel junctions
Cluster Novel type # Novel junctions # Novel junc. in splice site # Reads in cluster # Novel junc. reads Percentage [%]
case novel_acceptor 99769 58477 121889488 223557 0.18
case novel_donor 99769 41292 121889488 182588 0.15
control novel_acceptor 56579 32499 127058916 127074 0.10
control novel_donor 56579 24080 127058916 98371 0.08
Expand details
  • # Novel junctions: total number of novel junctions for that particular cluster.
  • # Novel junc. in splice site: total number of novel junctions for that particular splice site in the cluster.
  • # Reads in cluster: total number of reads from the BAM files that constitutes the cluster.
  • # Novel junc. reads: reads associated to the novel junctions in the cluster and splice site.
  • Percent [%]: the percentage that the novel junction reads represent to the total number of reads in the cluster.
\[ \text{Percent [%]}=\frac{\text{# Novel junc. reads}}{\text{# Reads in cluster}}*100\% \]